Predicting plasmids
===================

This section will cover:

* `Are there plasmids in Vibrio cholerae?`_
* `Predicting plasmids in your isolate`_.

Are there plasmids in Vibrio cholerae?
--------------------------------------

Plasmids can be an interesting and important feature of *Vibrio cholerae* genomes, particularly because
antibiotic resistance genes are carried by IncC/A-type plasmids in some isolates from the current
pandemic lineage (7PET). For example, the multi-drug resistant (MDR) phenotype seen in *V. cholerae* in
Yemen, starting in 2019, was due to spread of an IncC-type plasmid carrying antibiotic resistance genes
(`Lassalle et al 2022`_).
Therefore, understanding of evolution and spread of plasmids and other mobile elements in *V. cholerae*,
particularly in the current pandemic lineage (7PET lineage) is an important topic of research. 

.. _Lassalle et al 2022: https://www.biorxiv.org/content/10.1101/2022.08.24.504966v1

Many plasmids have been identified in environmental isolates of *Vibrio cholerae* 
(note that most of these isolates probably do not belong to the current pandemic lineage), as well 
as in isolates of the current pandemic lineage (7PET lineage) (see `De et al 2021`_). Some of these
*V. cholerae* plasmids have been given names (e.g. 'pVC1', 'pVC2', 'pSDH-1', 'pSDH-2', 'p3iANG', etc.).
Some of the classes of plasmids seen in *V. cholerae* are ColE1-like plasmids and Inc-A/C family plasmids (`De et al 2021`_).

.. _De et al 2021: https://www.frontiersin.org/articles/10.3389/fitd.2021.691604/full

Predicting plasmids in your isolate
-----------------------------------

If you learn better by seeing rather than reading, see the `video on predicting plasmids in H22, using Vibriowatch`_, for an example
using the assembly of the isolate H22 collected in Haiti in 2022, which was sequenced by `Rubin et al 2022`_.

.. _video on predicting plasmids in H22, using Vibriowatch: https://youtu.be/_mtfCiBlJac 

.. _Rubin et al 2022: https://pubmed.ncbi.nlm.nih.gov/36449726/

Vibriowatch uses the IncTyper tool to identify plasmids in *Vibrio cholerae* genomes.
If no plasmids are predicted in the genome of an isolate, you will see this in the 'Plasmid Inc types'
section of its report page:

.. image:: Picture99.png
  :width: 450
  
An example of an isolate with a predicted plasmid is RC9, which was isolated in Kenya in 1985.
Here is the 'Plasmid Inc types' section of its report page in Vibriowatch:

.. image:: Picture100.png
  :width: 650
  
This shows that this isolate is predicted by Vibriowatch to have a IncC-type plasmid.

CholeraBook
-----------

If you would like to learn more about cholera genomics, you may also be interested in our `Online Cholera Genomics Course (CholeraBook)`_.

.. _Online Cholera Genomics Course (CholeraBook): https://cholerabook.readthedocs.io/

Contact
-------

I will be grateful if you will send me (Avril Coghlan) corrections or suggestions for improvements to my email address alc@sanger.ac.uk